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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:GeDi.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings GeDi_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/GeDi.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘GeDi/DESCRIPTION’ ... OK
* this is package ‘GeDi’ version ‘1.4.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 29 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GeDi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  buildClusterGraph.Rd: igraph
  dot-graphMetricsGenesetsDT.Rd: igraph
  getAnnotation.Rd: STRINGdb
  getId.Rd: STRINGdb
  getPPI.Rd: STRINGdb
  getStringDB.Rd: STRINGdb
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘GeDi-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getAnnotation
> ### Title: Get the annotation of a STRINGdb object
> ### Aliases: getAnnotation
> 
> ### ** Examples
> 
> stringdb <- getStringDB(9606)
> stringdb
***********  STRING - https://string-db.org   ***********
(Search Tool for the Retrieval of Interacting Genes/Proteins)  
version: 12.0
species: 9606
............please wait............
trying URL 'https://stringdb-downloads.org/download/protein.info.v12.0/9606.protein.info.v12.0.txt.gz'
Warning in download.file(urlStr, temp) :
  URL 'https://stringdb-downloads.org/download/protein.info.v12.0/9606.protein.info.v12.0.txt.gz': status was 'SSL peer certificate or SSH remote key was not OK'
Error in download.file(urlStr, temp) : 
  cannot open URL 'https://stringdb-downloads.org/download/protein.info.v12.0/9606.protein.info.v12.0.txt.gz'
Calls: <Anonymous> ... get_proteins -> downloadAbsentFile -> download.file
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Error in `download.file(urlStr, temp)`: cannot open URL 'https://stringdb-downloads.org/download/protein.aliases.v12.0/9606.protein.aliases.v12.0.txt.gz'
  Backtrace:
      ▆
   1. └─GeDi::getAnnotation(stringdb) at test-downloadPPI.R:24:3
   2.   └─stringdb$get_aliases()
   3.     └─STRINGdb::downloadAbsentFile(...)
   4.       └─utils::download.file(urlStr, temp)
  ── Failure ('test-gs_histogram.R:27:3'): gsHistogram runs correctly ────────────
  `histogram` has type 'object', not 'list'.
  ── Failure ('test-gs_histogram.R:30:3'): gsHistogram runs correctly ────────────
  `histogram` has type 'object', not 'list'.
  
  [ FAIL 8 | WARN 13 | SKIP 0 | PASS 176 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/GeDi.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL GeDi
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘GeDi’ ...
** this is package ‘GeDi’ version ‘1.4.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GeDi)

R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(GeDi)

> 
> test_check("GeDi")
trying URL 'https://stringdb-downloads.org/download/protein.aliases.v12.0/9606.protein.aliases.v12.0.txt.gz'

preparing gene to GO mapping data...
preparing gene to GO mapping data...
[ FAIL 8 | WARN 13 | SKIP 0 | PASS 176 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-distance_dendro.R:11:3'): distanceDendro runs correctly ──────
`dendro` has type 'object', not 'list'.
── Failure ('test-distance_dendro.R:15:3'): distanceDendro runs correctly ──────
`dendro` has type 'object', not 'list'.
── Error ('test-downloadPPI.R:2:3'): no id ─────────────────────────────────────
Error in `open.connection(file, "rt")`: cannot open the connection to 'https://stringdb-downloads.org/download/species.v12.0.txt'
Backtrace:
    ▆
 1. ├─testthat::expect_true(is.na(getId(""))) at test-downloadPPI.R:2:3
 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─GeDi::getId("")
 5.   └─utils::read.delim(url(url_species))
 6.     └─utils::read.table(...)
 7.       ├─base::open(file, "rt")
 8.       └─base::open.connection(file, "rt")
── Error ('test-downloadPPI.R:6:3'): Homo sapiens ID ───────────────────────────
Error in `open.connection(file, "rt")`: cannot open the connection to 'https://stringdb-downloads.org/download/species.v12.0.txt'
Backtrace:
    ▆
 1. ├─testthat::expect_true(getId("Homo sapiens") == "9606") at test-downloadPPI.R:6:3
 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─GeDi::getId("Homo sapiens")
 5.   └─utils::read.delim(url(url_species))
 6.     └─utils::read.table(...)
 7.       ├─base::open(file, "rt")
 8.       └─base::open.connection(file, "rt")
── Error ('test-downloadPPI.R:10:3'): Homo Sapiens Misspelled ──────────────────
Error in `open.connection(file, "rt")`: cannot open the connection to 'https://stringdb-downloads.org/download/species.v12.0.txt'
Backtrace:
    ▆
 1. ├─testthat::expect_true(is.na(getId("Homo Spasiens"))) at test-downloadPPI.R:10:3
 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─GeDi::getId("Homo Spasiens")
 5.   └─utils::read.delim(url(url_species))
 6.     └─utils::read.table(...)
 7.       ├─base::open(file, "rt")
 8.       └─base::open.connection(file, "rt")
── Error ('test-downloadPPI.R:24:3'): PPI retrieval works ──────────────────────
Error in `download.file(urlStr, temp)`: cannot open URL 'https://stringdb-downloads.org/download/protein.aliases.v12.0/9606.protein.aliases.v12.0.txt.gz'
Backtrace:
    ▆
 1. └─GeDi::getAnnotation(stringdb) at test-downloadPPI.R:24:3
 2.   └─stringdb$get_aliases()
 3.     └─STRINGdb::downloadAbsentFile(...)
 4.       └─utils::download.file(urlStr, temp)
── Failure ('test-gs_histogram.R:27:3'): gsHistogram runs correctly ────────────
`histogram` has type 'object', not 'list'.
── Failure ('test-gs_histogram.R:30:3'): gsHistogram runs correctly ────────────
`histogram` has type 'object', not 'list'.

[ FAIL 8 | WARN 13 | SKIP 0 | PASS 176 ]
Error: Test failures
Execution halted